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Hi, I have a quetion about removing cnv like noise
First, I use Run_numbat(function) with option like this
`
out = run_numbat(
count_mat, # gene x cell integer UMI count matrix
ref_h…
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Hi @VPetukhov ,
I am trying to use DropEst with one of the 10x datasets from [here](https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/neurons_900).
I downloaded the BAM from…
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Hello,
Thanks for the great tool! Excited to test it out.
I am working with a 10X Multiome Multiple Myeloma sample. I ran the pileup and phasing script in the Docker with no problems, and exported …
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I'm running STARsolo on FASTq files that were generated from data off a NovaSeq X sequencer. It isn't generating any filtered counts, which I realized is because the barcodes.tsv and matrix.tsv files …
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For the BRCA dataset(breast cancer single-cell atlas), I can only get the raw UMI count matrix,
But in your paper, you present the true label of this dataset
,So how to download the true labe…
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**Describe the issue**
I am running the latest version of kb_python to reproduce the example pipeline in the BIVI paper (which was using an older version of kb_python). I generated the loom successf…
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Hi,
I am using the 0.48.0 version of kallisto, as well as bustools (0.41.0) to demultiplex and obtain gene count tables for my BD Rhapsody WTA data. This is my initial kallisto bus script:
**kallis…
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When running:
`soup_obj levels(soup_obj$Sex)
[1] "Male" "Female"
```
Seurat_5.0.3
EDIT:
I also get this when I try to use many levels:
```
Regressing out batch
Error in `contrasts leve…
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Hello,
With STAR version 2.7.10b, using STAR --runMode soloCellFiltering will not generate a Summary.csv file containg informations relative to the cell filtering that we can found if we launch STA…
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I was trying to get count matrix from 10x fastq files. I got this fatal error notification saying "**--soloUMIdedup=1MM_CR is not allowed for --soloType CB_UMI_Simple**".
Here are the parameters I a…